The Last Ship Season 2
by queenpearl
Summary: The second season of the Last Ship. Updates weekly.
1. Chapter 1 Unreal City

Nathan pushed his weight against the side of the metal cage holding him, trying to find a way to escape.

"It's no use." New York sighed behind him. "They've got you strapped down like a monkey in a cage."

"I don't appreciate that analogy, sweetheart."

New York winced at the venom in his voice. "I'm sorry. I did try to warn you. I told you to leave."

"Leave and leave you here in this hell. Out of the question!" He snarled, ramming the dock again. This time the ropes slackened, just a bit but it was enough. The new management on board also got a good toss and Nathan felt some measure of satisfaction. He got a stinging swat to the side.

"Quit that!" The man snarled.

"Not on your life you cowardly son of a bitch!" Nathan spat back and rammed the dock again. The man fell overboard and got mooshed between Nathan's hull and the dock. "Serves you right." The ship snorted. He turned his attention back to New York. "I want out of here. You with me?" He asked.

"Nathan, it's impossible." New York whispered.

"No it isn't!" He replied. "I've been doing the impossible for months now."

"If you can promise we can get out of this hell hole and put a dent in Granderson's operation, then yes!" She growled.

Nathan nodded and turned his attention back to the commotion on his bridge. Quincy had been shot and the doc was doing what he could to help. Nathan bit back his whimper of worry, determined not to give these men any excuse to find leverage over him.

The men were yelling about the primordial which they required to make the cure. "Dr. Scott is pregnant. We can use the stem cells from her unborn child to make a strand."

That was the last straw for Nathan. He reared up in the cage, nearly flipping as his mooring lines groaned under the strain. "If you dare even touch her." He snarled. "I'll give you the longest, most painful death there is!"

"Ooh someone's protective." The lead man sneered.

"Her baby, the stem cells won't give you the cure you're looking for." Nathan growled.

"No and why would that be hmm?"

"Because..." Nathan began but paused as he caught the gaze of his mate. The betrayal and hurt in New York's eyes told him she knew. She knew what he had done.

"Because the child's a hybrid." He growled. "It's only half human. I'm it's biological father."

The man growled and gave Nathan a good smack, causing the warship to drop back down, slamming his side into the cage.

"I want that primordial strain and I want it now!" The man roared.

Panting, Nathan gazed up at New York. "It only took you the end of the world to find someone else?" She asked him. "Without knowing for certain if I was dead."

"New York, I-I'm sorry." He whispered.

She looked away, head bowed. She refused to even meet his gaze.

Shouting brought Nathan back to the commotion inside him.

The men were shouting at the injured Quincy. "Where is it?!" The lead man demanded.

"I-I told you. I don't know." Quincy groaned.

"But I do." New York but in.

Nathan sent her a questioning look. No way could she know anything. She blinked at him but said nothing.

"New York?" The men turned to her, weapons raised.

New York glanced at her mate, a silent message in her eyes. _"Be ready to run."_

And that's when Nathan understood. "New York, no! You can't do this! Just give them what they want!" He cried.

New York ignored him and turned her attention back to the men.

"Where is it, New York?" The lead man asked, weapon raised to shoot her brains out.

New York hesitated, her eyes closing briefly. Deep within her missile bay, a charge was set.

"I'm sorry, Nathan. I love you." She whispered.

"New York..." Nathan began.

"You'll never find it!" New York snarled to the man and the charge detonated.

New York was killed in an instant, erupting in a ball of flame. Nathan cowered as debris rained down, the lock on his cage becoming damaged to the point where he could break free. And break free he did, rushing out to find the remains of his mate sinking to the bottom of the harbor.

"New York." He whispered, his voice full of grief. "What have you done?"


	2. Chapter 2 Fight the Ship

Nathan was filled with a new resolve as he fought against the men holding him captive. Bullets rang off his steel skin from the pair of choppers circling above him. A crewman took out one of the birds with his AA guns and Nathan cheered. Eyes zeroing in on the city, Nathan picked up on Chandler and his team. They were well on their way to taking the building. Nonetheless, Nathan had a weapon trained on their location just in case.

Shaffoty, the XO, was busy in Comms, watching his boys take the CIC. "Ha!" Nathan laughed. "That's my boys!"

His happiness was short lived as the remaining chopper let loose with a missile that struck Nathan upside the head, blowing half his skull off. The warship screamed and fell on his side, oil everywhere.

"NATHAN!"

Dr. Scott's voice shook Nathan from his fog. He tried to stand but couldn't, falling back on his side. He tried to speak but the muzzle prevented him.

"Nathan..." It was Chandler. The captain knelt on the dock and ever so gently removed the muzzle. "I'm never leaving you again." He promised.

Nathan pressed his nose to his hand, whimpering. The fog surrounding him prevented him from doing much more. He coughed weakly, trying to dispel the acrid taste of oil in his throat.

"Hey, stay with me here. Nathan, come on. I need you to focus." Chandler begged, his tone becoming more urgent.

Nathan tried, oh he did try but he was fighting a losing battle. His eyes closed and his nose landed in Chandler's lap as darkness took over him.


	3. Chapter 3 It's Not A Rumor

"Oh my god!"

"Nathan!"

Nathan's head was filled with fog. He groaned weakly and stretched his nose out, sensing his captain's presence was near.

"I'm sorry.." he rasped.

"For what?"

Nathan felt Chandler's hand on his nose.

"It's okay Nathan. I'm here." He said.

"Where am I?" Nathan murmured, unable to open his eyes for some reason.

"Norfolk, we took control of your engine plant and sailed you here." Chandler replied.

"Arleigh? Is Arleigh here?" Nathan asked, trying to raise his head.

"Shh, yes. Yes he's here. He's fine. Dr. Scott gave him the vaccine." Chandler replied.

Nathan sighed in relief, visibly relaxing. "Our boys?" He asked.

"A skeleton crew is on board, attempting to repair the damage you suffered. The rest is out searching the city." Chandler replied.

"What's the damage, captain?" Nathan asked.

"You took a shell to your skull. But you got lucky. It only took out your hull. The wiring's all been replaced and welding should begin tomorrow. You'll be cleared for duty by the end of the week." Chandler replied.

"Mm. That's good to hear. Why-why can't I see though?" Nathan asked.

"Cloth over your eyes. A safety measure." Chandler replied.

Nathan nodded. He was notorious for going stir crazy if stuck in the same place for long periods of time. Putting a cloth over his eyes was a safety measure. If he couldn't see, he was less likely to lose it and try to escape.

"How's everyone's holding up?" He asked.

"Some found their families and some..." Chandler broke off but Nathan nodded, he understood.

"New York. She sacrificed herself for me." He said.

"I know. I saw the explosion." Chandler murmured, his voice carrying sympathy. "Nathan, there's something I have to tell you."

"I'm listening captain." Nathan replied.

"I'm resigning my commission. You know what people out there are willing to do to get the cure and as long as we're leading the mission we're a target. I will not risk having my judgement affected because I'm worried for my families' safety." Chandler said.

"NO!" Nathan roared, so loudly that all ships looked over at the pair. Nathan righted himself. "You will not resign! I won't let you!" His teeth were bared and behind the cloth, his eyes blazed with fury. "We've come so far, we can't give up now. The crew needs you, I need you!"

"And they don't!" Chandler retorted. "What if I don't come back and make those kids orphans?!"

Nathan sighed and thought for a moment before replying "You think you aren't the first soldier who had to leave his family behind? Royal Naval officers put their wives and children in bunkers in London while they went to fight the Nazi's, for years!"

"Wives and children. The wives were there..." Chandler murmured brokenly.

"I know you. And I know you're beating yourself up but if you're looking for someone to blame, blame me." Nathan growled. "I should've come right back as soon as I'd learned something. But don't trip on yourself, there's no time for it. Whether you like it or not, you're Noah and I'm your Ark." To the controller he growled "Open the gates."

The drydock was flooded and Nathan angrily stormed out into the harbor, leaving his captain behind at the dock. But the message got through. Chandler, with new determination in his eyes, gazed after him. "Alright then."

He rejoined Nathan farther down the dock. "You were right." He said. "I was wrong, I'm sorry."

Nathan leveled his gaze on him. "We're in this together now, until the end."

"Until the end." Chandler agreed. He stroked his ship's nose before climbing aboard. Dr. Scott joined him on the foredeck. She was showing signs of advanced pregnancy. "How long?" Chandler asked.

"Any day now." Dr. Scott replied.

"The surgeon ready as soon as you go into labor." Chandler said. Nathan shifted underneath them nervously.

"I'll be fine." Dr. Scott assured him and the ship relaxed.

Nathan weighed anchor and on his way out he passed Arleigh. "Good luck little brother." The older ship said.

"You too." Nathan replied, nuzzling him.

Arleigh watched him until he vanished over the horizon.


	4. Chapter 4 Solace

Nathan knew something was up the minute he found USHS Solace. The hospital ship looked fine physically with no traces of the virus on her. She was lucky there.

But as soon as she saw him coming towards her she cried out "Nathan stop! No! It's not safe!"

"You don't appear sick." He said, pausing in his course.

"It's not the virus. They-they thought I had the cure. They've taken my crew hostage. There were gunshots. I fear-I fear they killed them." She whimpered.

"Attacking a hospital ship is in direct violation of Geneva." Nathan growled. "I'll make them pay, Solace. I swear."

She bowed her head. "Just be careful." She whimpered. "These guys aren't amateurs. When they came here aboard a submarine, I..."

Nathan cut her off. "Submarine?!" He exclaimed.

She nodded. "I saw her sail. She's Royal Navy." She replied.

"Damn. Just what I need." Nathan groaned.

His destroyer instincts began to come to life. For any DD a submarine meant only one thing, danger and death. They were natural enemies, and had been since their creation. A submarine was a destroyer's natural predator and it took all of Nathan's willpower to remain at Solace side rather than run to the nearest port, out of the sub's reach.

"Where is this sub?" He asked, his voice tense.

"I don't know." Solace whimpered. "I saw her briefly and then she vanished. Be careful Nathan. She's a sneaky one."

"I consider myself warned." He assured her and lowered his small boats.

A voice came over the radio. "US Navy. Be warned, we can and we will make you surrender." It carried a distinctive British accent, which was surprising.

"USS Nathan James here, identify yourself!" Nathan snarled.

Silence greeted him and with a frustrated snarl, Nathan whacked his bow on the water.

It wasn't long after that Shattery got a call from Chandler, telling him of the planned ambush on the enemy combatants, whoever they were.

Nathan's small AA mounts twirled around and aimed on the door on Solace's top deck in preparation for the ambush.

"We have to get in closer to be in range." Shattery said.

"Sir, any closer and we'll collide!" Nathan called.

"I don't care!" Shattery growled. "Bring me in closer. Find me something to shoot!"

Nathan revved his previously idle engines. "With pleasure."

When the first guy appeared, driven to the open deck by Chandler's gunfire, Nathan didn't wait for the gunner to shoot. He took control himself and pounded the man's guts full of lead.

"Oh yeah!" He cried. "That's what I'm talking about!"

The other two popped smoke to hide their retreat.

"These guys are good." Nathan said to Solace.

"I did warn you." She whimpered. She looked very, very afraid.

"Solace, what is it?" Nathan asked. "What's wrong?"

"My-my engine room. They've rigged it. Remote detonator." She replied.

Nathan gasped. "Everyone off Solace, now!" He roared through the comms.

"Make way!" said a familiar voice. It was Tex. Nathan saw him running across Solace's deck, carrying something.

Up on her bow were Chandler and another guy. He wasn't sure who but he had a feeling it was the guy who was behind that voice he'd heard earlier. He held a detonator in his hand and suddenly everything made sense to Nathan.

"Down now!" He roared to the officers on his bridge just as the button was pushed and Tex threw the detonator over the side. It exploded harmlessly in between the two ships as the detonator man leaped over the side and didn't come up for air. Only a shower of bubbles appeared and Nathan had a feeling he knew what they were.  
Nathan smiled. "You're welcome." He replied.

"Who were those guys?" He asked Chandler.

"I don't know. But that guy didn't come up for air." Chandler replied.

"I know. I'm getting the distinct feeling of being watched. Every instinct I have is telling me to run. I'm a destroyer so you know what that means." Nathan said.

"You're the deer being watched by the cougar." Chandler murmured.

"We'll find that sneaky bitch. We will!" Nathan growled.


	5. Chapter 5 Achilles

Nathan could sense the sub was still around and was stalking him. He could feel it in his bones.

 _"I have to get out here."_ He thought as he engaged his engines.

His sonar detected the submarine as it followed him. Experimentally, he turned slowly to port, curious to see if the sub was listening or not. Turns out she was.

"They're turning with us sir." He reported.

"Damn. All hands prepare for Quiet 2!" Chandler ordered.

"Sir?" Nathan questioned.

"They can't track us if they can't see us. Quiet 2!" He repeated his order.

Nathan complied, slowing his engines. Running at Quiet 2 he made his way at an agonizingly slow four knots to the shoal nearby. He hoped the shoal would hide him long enough to fire off torpedoes into the sub.

...

Achilles cursed her luck when the destroyer disappeared off her passive sonar.

"Running at Quiet 2, clever." She chuckled.

Her sensors picked up a shoal nearby.

 _"If I was a destroyer who wanted to fire a few fish into a sub without said sub finding my hiding place, I'd go there."_ She mused and changed course accordingly.

...

Nathan heard the sub changed course and growled in frustration. This was a clever sub. Quietly, he began a 20 degree turn to port out of the shoal, in 5 degree increments, at random. If the sub decided to fire torpedoes now, she wouldn't know where to aim them.

He thought hard about the sub. Royal Navy submarines weren't known for stealth such as this. Unless of course, they were being upgraded. Only one though matched this sub.

"The sub is an Achilles class." Nathan said.

"Understood." Chandler replied.

 _"Of all the submarines in the world. I had to get one that's nearly as silent as one of our own!"_ Nathan thought to himself.

...

Achilles was quickly growing impatient. When her lunatic of a crewman took over, he'd promised her battle. He'd promised her blood, appealing to her natural instincts. So far, he had yet to deliver.

"Patience, darling." He purred dangerously. "Endless patience is the key."

Achilles growled, green eyes narrowing into fine little slits. "You promised." She accused.

"And I will soon deliver but we must be patient. This destroyer will not be an easy target." He said.

She reluctantly conceded. "We need to find them first though. We could if we could go active." She said.

"They'd see us though!" one crewman cried.

"Assuming they haven't already!" She shot back. "Captain, what do you say?"

The man was silent for a moment before nodding. "Do it!"

...

"Sir they've gone active!"

Nathan's blood ran cold at this. While he could easily pick up the sub's acoustic signature now it also meant torpedoes were soon on their way. Submarines only used their active sonar as a last resort.

Growling, he turned hard to starboard, engaging his engines to full speed, and launched 3 torpedoes over the side.

...

Achilles heard the fish as soon as they entered the water. "Damn that tin can!" She snarled and launched 5 of her own.

...

Nathan saw these on his sonar and fired more, using the torps' bearing to locate the sub's position. He made a hard turn to starboard, crossing over his wake to confuse the torpedoes as they came in.

...

Seeing the ordinance coming her way, Achilles snarled and immediately dived. She dived fast and deep too. An underwater canyon, barely big enough for her to fit, loomed ahead. Making a slight roll to starboard she managed to force her bulk into it.

"Ooh I really regret taking those human dinners now!" She grumbled as she tried to make the tight fit.

"Suck it in Achilles!" came the cry.

"Shut up! I'm working on it!" She growled back.

She'd just slipped through the canyon when the torpedoes flew by harmlessly overhead and realizing they had no target, detonated harmlessly.

Despite herself the sub chuckled. She may not have gotten the destroyer today, but she still had one last card to play.

...

Nathan recognized the sound of missiles firing at once. 26 in all. They were heading straight for the lab coordinates marked on his map.

Swiftly he countered with his own but only managed hitting 2. The rest were out of range. He gave the order for the labs to evacuate to at least a 2 mile distance. He wasn't sure if the message even got through.

"They don't want the cure." He realized.

"They want to destroy it." Chandler finished.

"A new race of superhumans. Immune humans." Dr. Scott whispered.

"Now why does that sound familiar?" Nathan grumbled. Clearly someone hadn't learned the lessons of history and Nathan vowed he'd do everything in his power to ensure this newcomer remembered them!

...

Achilles' hull was feeling the pain of the rocks as she bumped them. She was stiff, sore and tired. Before this whole mess began she was scheduled for 10 months maturity leave. Now she could feel her unborn shiplings bounce around inside of her.

 _"Calm little ones."_ She murmured in her native tongue. She couldn't risk revealing them to her madman of a captain. He'd just as soon terminate her pregnancy and then her.

Despite her pain, Achilles still felt the rush of battle in her ears. It was an exhilarating experience. Her highly tuned senses detected traces of blood in the water, apparently someone on board had been injured, their blood being washed from the scuppers. Her tongue flicked out to taste it and the submarine purred appreciatively.

"Let the hunt, began!" She chuckled.


	6. Chapter 6 Long Day's Journey

Nathan James waited impatiently offshore of the Florida swamps as his captain led an away team ashore. Their mission, avenge the people who killed Dr. Scott's close friend, Dr. Hunter.

The destroyer thought back to the moment when they'd learned of his tragic death. Not by missiles like the other labs had been, but by armed militia.

...

Nathan hadn't seen Dr. Hunter's prone body but he'd heard the video. And he'd heard Dr. Scott beg of the captain that when he found the people who did this, to kill them.

"Keep a close eye out. If you see anything suspicious, shoot it!" Captain Chandler ordered.

Nathan bobbed his head. "Understood sir." He replied.

...

He hadn't heard from the captain in hours, not since they'd gone radio silent just outside a compound that they believed to be housing the militia that attacked the labs. As Nathan tried to establish contact with them he heard another signal coming from nearby.

It was coming from a buoy 20 miles east of his position.

 _"That sub's using buoys to signal her crew ashore, clever."_ He thought. Out loud he added "But not clever enough to fend off this!" He fired a missile and got conformation of the destroyed buoy!

...

As soon as the comm-links went dead, Achilles knew what had happened.

"Clever, clever boy." She chuckled. She debated whether or not to tell Sean but decided against it. The man was insane and would kill Nathan without a second thought. Achilles wanted that honor to herself. She made a fateful decision and kept silent.

"Until next time, Nathan James." She said.


	7. Chapter 7 Alone and Unafraid

Nathan was chomping at the bit practically as he listened for Vulture Team's update.

"Come on Chandler..." He whispered. "Please..."

Slattery was just as impatient. "Extraction point's a baseball field about four klicks North of the compound according to Green team." He said, relaying the message.

"Big enough for our hilo." Nathan murmured.

"Get a fix on it!" Slattery ordered.

"Already on it sir." Nathan replied, working the description through his computer. "Got it! Can we launch it now?"

"Not with that sub out there, it'll hear us." Slattery growled.

"Damn, where can we go that we can launch without being detected?" Nathan asked.

"Mouth of the St. Johns River would be the closest. Set a course there, Quiet 1, 12 knots." Slattery ordered and Nathan did so.

"Damn, I think you actually missed an outcropping." Achilles grumbled, rubbing her side with her port plane. She was in a foul mood for she had emerged from the canyon with a bowache that was only getting worse. Part of her morning sickness. She hadn't actually thrown up though, yet.

"Ah quit your bitching!" the quartermaster snarled, a bit African in a British tank.

Achilles huffed but she knew better than to keep talking. Her eyes flickered to her sonar panel. It beeped. She had a new contact. Still though, she said nothing. She would let the crew find it for themselves.

They saw it a few minutes after she'd seen it. "It's that destroyer!" cried one. "We should sink him now. It's what Sean would want."

"No, it's what Ned would want!" retorted the quartermaster.

A big argument broke out and Achilles felt her headache turning into a migraine. "SHUT UP!" She roared. "ALL OF YOU WANKERS JUST SHUT THE FUCK UP!"

They all stopped in shock. "Damn, I just need to think." She groaned. "Without your bickering giving me a migraine."

...

"Sir, we've got something on sonar. It's faint but it's there." reported Lt. Foster.

"Is it the sub?" Slattery asked.

"Affirmative sir. It's traveling fairly quickly, close to the surface. The draft on it is too big though, it can't follow us into the river."

"She." Nathan interrupted.

"Something you care to add, Nathan?" Slattery asked.

"That submarine's a she." Nathan replied.

"How do you know?"

"I just know. It takes a ship to understand another ship."

Slattery merely huffed in reply.

With her few minutes of silence, Achilles had time to think. Her pregnancy was becoming more pronounced by the day. Her sides were widening to accommodate the 12 unborn pups within her. It wouldn't be long before questions were asked. The quartermaster, if he found out, would kill her for sure. As would Ned. Sean, maybe not. A fleet of submarines could be useful and their breed grew quickly too. They could be pressed into service at age 2 but could prove to be helpful as yearlings. For the time being though, Achilles needed the attention off her. She made her decision.

"Go active sonar." She ordered.

"They'll hear us!" came the retort.

"If they haven't yet?" She snapped back. "Do it, now!"

...

"We're being pinged!" Nathan shouted, feeling the vibrations along his hull.

The water was so shallow that the submarine would have to be close to the surface to fit without running aground. Looking, he could just see the tip of a leopard spotted periscope. "There you are, you bitch." He chuckled. He armed his weapons though he wouldn't dare fire unless she fired first.

It was a waiting game. A dangerous game of cat and mouse and Nathan prayed to Poseidon he was the cat.

...

Achilles was forced to retreat when Nathan disappeared off her sonar as he entered the St. Johns River. "He's a slippery one." She murmured, her tongue swiping itself around her jaws once. "It will be a pleasure to sink him eventually."

"You could've sunk him now! Why hesitate?!" The quartermaster snarled. Before she could answer, he struck her Conn hard.

Achilles shrieked and rolled on her side, striking bottom. She gasped as she felt ripples of pain work their way down her side. Big mistake, coughing as she worked to clear her lungs, she blew herself to the surface, bursting from the water like a whale. Jaws parted, she took in the air gratefully.

The crew sat in total shock, a few giving the quartermaster murderous looks. Several were former navy enlisted men. They knew and understood to respect their ship and she in return would bring them home safely. One man moved from his position, heading for the hatch.

The quartermaster drew a gun on him. "Stay where you are!" He snarled.

The man held his ground. "You've hurt her. I must see if she's okay." He replied.

Reluctantly, he was allowed to leave. Emerging outside, he crawled his way forward, to Achilles parted jaws and lolling tongue. The sub's sides gleamed with oily sweat and they heaved as she fought to regain her wind. "He shouldn't have hit you." He said.

"I deserved it." came the automatic reply. Achilles' voice was blank, her tone nonexistent.

"You don't believe that and I don't believe it either. You did the best you could." He said. "But he did have one question right. You had all the time in the world to fire, why didn't you?"

Achilles sighed and looked at him. The man was a former British Royal Navy Chief Petty Officer. He could be trusted to keep his mouth shut. "Because I don't just have my life and your lives to consider." She rasped.

His eyes widened slightly as he understood the message. "How long?" He asked.

"I'm nearly a year into it. I've got a few more months to go, then..." Achilles broke off with a wince but he understood. Then she would give berth to a dozen pups and both would pray Sean would not kill them immediately.

"I won't say a word." He promised.

Achilles relaxed considerably at that. "Thank you." She murmured.

"You look pale." He commented.

"Morning sickness. I think this time I'll throw up." She replied, starting to retch.

"I'll tell the crew you've got a stomach bug." He said.

"Thanks." She murmured.

"Be right back." He promised, giving her hull a pat.

As soon as he went back inside, Achilles gave into her body's demand and proceeded to puke her guts out.


	8. Chapter 8 Safe Zone

Rachael was hard at work in her lab and Nathan was busy listening to the radio chatter from his captain. He was returning aboard with the Commander in Chief. As the boat approached, Nathan straightened up and raised his bow and guns in salute. He was mostly ignored but he got a slight nod from Michener in return. That made him feel a little bit better.

Chandler updated him on recent events.

"He's WHAT?!" Nathan cried, not quite believing what he was hearing.

"The President's an Immune. He's been brainwashed by the Ramsey's. It's our job to set things straight." Chandler replied.

Nathan sighed. "I-fine.." He sighed.

...

Achilles groaned as she felt her shiplings bounce restlessly within her. They were growing fast and as a result her hull began to widen at an increasing rate. No one said anything but it was an accepted fact that she was pregnant. The submarine sighed. She'd received news of Nathan's recent attack. One of his crew nearly killed Ned. Achilles wished he'd been a little more accurate with his shot. She wouldn't have missed him if he had been killed.

For not the first time since this whole mess began, the Immune sub wished for redemption. Some way out of this mess. No more bloodshed, no more lies and hate. Most of all she wanted a safe place to raise her shiplings. As soon as they were born she planned to take them to Nathan to be vaccinated. Just because she was immune didn't mean they would be. What's more, she planned to leave them with the destroyer. A cruel choice but one that had to be made. When Sean had found out that she was pregnant just hours earlier he'd screamed and ranted at her, swearing he'd kill the pups as soon as they were born. Achilles knew he'd keep his word and she was counting on Nathan to prevent him from that.

 _"Please..."_ She thought. _"Please Nathan, help me.."_

 _..._

In Nathan's on board lab, Rachel dropped the equipment she was working with, groaning as water pooled at her feet.

"Nathan..." She gasped.

The destroyer was on alert at once. "What? What is it?" He asked.

"It's coming." She replied. "Our baby is coming now!"


	9. Chapter 9 Uneasy Lies the Head

With the doctor on one side and Chandler on the other, Rachel was helped into sickbay and laid on a hospital bed. She groaned in pain as contractions seized her. Nathan wasn't helping.

The destroyer and father-to-be was shifting his weight constantly, worried for his wife's safety. Eventually, Chandler had enough.

"Nathan, quit fidgeting and be still!" He roared.

Nathan instantly complied. It wasn't worth a pop on the butt and Chandler knew how to deliver one too. His still sore stern could attest to that.

"God damn it!" Rachel swore. She'd helped delivered hundreds of babies but now she pitied all those mothers. Giving berth sucked, period!

"Push Rachel push!" Chandler ordered.

The WHO doctor did, gasping for breath as her chest heaved, sweat gleaming on her forehead.

Night began to fall and still no joy. Rachel was still struggling. Eventually, the doctor decided to perform a C-section. This baby simply would not come out on its own. It was also likely that Rachel's passage was too narrow for it anyway, due to its half ship heritage.

Rachel was put under and Nathan tugged on his anchor nervously. He was eager for this baby to be born and at the same time, fearful for his wife's safety. He knew the risks of such a union. Rachel could easily die from a childbirth like this. Ships weren't meant to be born out of humans, and humans weren't meant to carry them to full term, simple as that.

Eventually, the baby was located stuck halfway between the uterus and the canal. It was too big to be born normally. Chandler gently removed it from the sack and gave it a sound smack that made even Nathan wince to get its lungs working. And what a pair of lungs they turned out to be too.

The shipling's wail sounded throughout the ship, making everyone stop and look up. A few offered their congratulations and patted Nathan's bulkheads.

The newborn had his father's look. He was clearly an Arleigh Burke-class destroyer. At a mere 60 lbs he was a runt but Nathan supposed that had to do with his half human heritage. His mast was flat to his back to protect itself as it grew, the little radar mast already fully functioning. As typical of a shipling, his eyes remained closed and his hearing almost none existent. He went by feel alone. His little props, no more than little points of flexible jelly (they would harden over time), tickled Chandler's chin as he lifted him up high.

"Congrats Nathan." He said after a moment. "You have a son."


	10. Chapter 10 Friendly Fire

As Nathan headed for New Orleans his attention turned to his wife Rachel, and the little bundle she was holding. Chandler Scott-James was now a week old. His eyes had opened and it turned out that he had his mother's deep blues. Everything else he got from his father and unfortunately that included a ridiculous pranking and exploring streak.

From the time that he could flop about Nathan's deck and passageways, the shipling was a first rate troublemaker. He was barely the size of a human teenager so he could fit just about anywhere the crew couldn't, making him the expert at sneaking about. The cooks were his favorite victims. Steal a few of their apples and they'd be on the rampage looking for them. One time Chandler even set up a beer trap for them. During the night he rigged a keg of beer that he'd found down in the hold so when the cooks came in the galley the next morning, their yelling and swearing was heard throughout the ship before they staggered out soaked in Bud Light.

But Chandler's eagerness to explore could also get into trouble. This became a frightful reality one day.

Captain Chandler was off on a shore mission, rescuing a group of teenage boys from a bad neighborhood. Rachel was working in the lab alongside her and Nathan's worst enemy (besides the Ramsey's) Neils. Chandler was curled up fast asleep in the crib just outside. The shipling had been vaccinated the moment he was born. Rachel had created a special string of the vaccine for ships which Nathan was glad of. He wondered, not for the first time, how many of his kind were left roaming the seas.

A few hours later, Chandler woke up. He wasn't hungry, he'd been fed fairly recently. Eating could wait. Looking around him, the shipling marveled at all the shiny sparkling medical equipment. He had to get closer and touch one of them. He found he could slip through the bars of the crib and did so, landing flat on his belly on the tile floor. Finding a leg of a table within reach, he used a rigging wire and pulled himself over to it. Then did the same with the next object he could reach. He did this until he bumped into something hard but warm. A human leg. Looking up with a surprised cheep, Chandler saw a pair of brown eyes meet his.

Neils regarded the little shipling with a mixture of jealousy and hate. _"That should be my son."_ He thought. _"Rachel should've been my wife, not this tin cans!"_

His anger ruling him, Neils picked up Chandler and regarded him. "Been vaccinated little one?" He sneered. "Let's find out?" He breathed on the little shipling and Chandler squeaked in disgust at the foul smell of his breath. Then Neils found a needle filled with a primordial and jabbed the tip into Chandler's shoulder. The shipling squealed, fighting him.

This alerted Rachel who launched herself across the lab and bowled Neils over, jabbing an IV filled with DNA splicer into him. The virus took effect almost instantaneously and Chandler watched as the man drowned in his own blood, despite Rachel's efforts to cover his face. She took the needle out of his shoulder (thankfully none of the primordial had entered his bloodstream) and placed him back in his crib.

"Stay there!" She ordered sternly.

Chandler cheeped once in reply. He knew not to disobey his mother when she had that tone in her voice.

...

When Captain Chandler returned and learned that Neils was dead, he was furious. How could he be expected to beat the propaganda campaign the Ramsey's were playing without him.

He confronted Rachel, who admitted to her crime.

"When we make safe port, I will turn you over to civilian authorities, and you will answer for you crime." He said.

Nathan snarled in fury.

"Something you care to add, Nathan?" Chandler asked.

"She was protecting our son, _your namesake!_ Neils was going to kill him!" Nathan replied with barely constrained rage.

"Nonetheless she committed a crime and she must answer for it." Chandler replied.

"When we make safe port." Nathan hissed, voice dangerously low. "It won't be Rachel who walks down that gangway. It will be you, in a body bag! **I will DIE before I allow you to seperate my family!"**

With that captain and ship separated. They were forced to work together still for they still shared a common goal in saving the world. But once that goal was met, neither intended to speak or see each other again. They'd made their own choices, and gone their separate ways.


	11. Chapter 11 Valkaryie

Nathan hated her! He hated the woman who had framed him for murder. Approaching the oil rig he was ready for battle, he was ready to take her on! He didn't realize how costly this battle would be.

His away team led by his captain surrounded the rig before boarding. No one except her, Val, was found. Val tried to escape and from there things went sour.

First a civilian yacht fired a RPG at the oil rig, rupturing gas lines. Then the thing blew up. Then at 3 people were KIA. And then Captain Chandler collapsed. Captain Chandler...

Nathan was surprised at the regret he felt. Regret, fear, pain at what he'd said and done to that man before this mission. He regretted it all, and now he feared he'd never have a change to atone for it. Thank Poseidon for Dr. Scott. Her quick thinking may've saved Chandler's life.

Speaking of Chandler, Nathan's son managed to wriggle his way around the flight deck until Slattery picked him up and moved off into a corner so he wouldn't get under foot. The shipling was naturally curious and whined and wailed for his mother.

"Nathan, can you handle him?" Dr. Scott asked.

"Yes." The destroyer answered.

Slattery dropped him in the water and Chandler squealed at feeling it for the first time. He slapped at it playfully, giggling all the while. His bright blue eyes, the only inherited feature from his mother, sparkled with mischief. Nathan could only grown inwardly at the thought of all the trouble he would cause. As it was, Chandler merely cheeped and found his way to his father's side where he cuddled up cutely.

"I'm sorry you couldn't hang out up there." Nathan said. "But that isn't the best place for you right now."

Chandler cheeped curiously.

"Your namesake, my captain, he's injured. Him and several others. Your mother is trying to treat them and she thought it best that you come here. For your own safety." Nathan said.

Chandler didn't understand half of what was being said to him but he cheeped and nuzzled his father anyway.

"Aww, come here you little rascal." Nathan laughed and held the shipling.

...

Captain Chandler woke from his unexpected sleep a few hours later. He was lying on his back in his stateroom bed. Dr. Scott was hovering over him. She breathed a sigh of relief.

"You were touch and go for a while there. Some of us thought we'd have lost you for good." She said.

He groaned. "What's the damage?" He asked, trying to sit up. She pressed him back down gently.

"Well you lost a lot of blood and I still have to go in and remove the shrapnel that is called home behind your liver." She said. "At least I can still use my powers for good."

The jibe was subtle and Captain Chandler winced but he knew it was well deserved. "It can wait." He said.

"No, I'm afraid it can't." Dr. Scott replied. "The shrapnel could move and cut you."

"I'm fine." He said.

"Stubborn as ever." Dr. Scott sighed and turned to go.

"Rachel?"

Nathan was surprised and so was Dr. Scott who turned around at once. Captain Chandler had never called her by her first name.

"Thank you." He said.

Dr. Scott nodded and left.

 _"Reconciliation indeed."_ Nathan thought.


	12. Chapter 12 Cry Havoc

Achilles could care less about the so-called "destroyer sightings" along the coast. She knew they were fake. She knew Nathan had captured Val and was now using her to trick the network. But she didn't tip the Ramsey's off to this. In fact, she could care less about them or anything else at the time. The submarine groaned as she felt the beginnings of a contraction seize her. It was 30 minutes earlier that her water had broke. She was going into labor at the worst possible time. She was going into battle as she gave berth!

...

The water smelled funny to Nathan as he emerged from the mouth of the river and into the open sea. Not a toxic funny just, funny. He knew the smell from somewhere but he couldn't place it. He shook his head, now was not the time to be thinking about trivial things. He had a submarine to catch!

He killed his engines and drifted into the predetermined battle zone. His dance partner had yet to arrive though. What was taking her. His makeshift sonar saw nothing, then. A ping revealed their position...

"Son of a..." Nathan swore.

...Right under him!

Achilles detected him in the same instant and rose to the surface. Nathan swore again and accelerated, she with him. He was forced to disengage the safety features on his engines which kept them from revolving too fast. But he had no choice now. He needed all the speed he could get. Up ahead his sonar detected a deep trench. Achilles would fire her torpedoes and then dive. He had to make a move before then.

As she reached the edge of the trench, Nathan reversed his engines suddenly, creating a spectacular roostertail behind him. His torpedoes were launched and he confirmed at least 1 hit though he wasn't sure if Achilles was sunk or not.

The sub screamed as she felt the impact. Within her womb she felt her pups shift, their little bows and props digging into her flanks. She pulled up from her dive, heading for the surface as she left a trail of blood behind her.

300 yards astern of Nathan the water shifted and up came Achilles. The submarine was in bad shape, her port quarter dented inwards and mangled. She whimpered in fear and pain, barely able to get up enough speed to come alongside Nathan who had his teeth bared and guns aimed at her. The destroyer seemed unflinching and Achilles submitted herself to whatever fate awaited her. Pregnant or not, she was a ship of war and she had lost.

Nathan's nose twitched and his eyes widened slightly as he finally recognized the funny smell for what it was. Water and not just any water, water from a womb that had just broke. Eyeing Achilles' severely widened sides he knew.

"How many?" He asked her.

"A-A dozen." She replied. "Please!" She begged, crying out as a contraction seized her. She rolled on her side.

Nathan sucked in a breath. The damage to her stern prevented the pups from safely traveling down the passage but it was too late now to do anything about it. The pups were already on their way. Achilles shrieked in pain as the first one collided with the blocked region. Behind it the other pups waited, impatiently. The line built up and with a sudden pop and flying of hull plates, Achilles' dent came undone. The submarine screamed, pushing hard as her tongue lolled between her teeth. In a fountain of blood the first pup emerged, swimming doggedly to the surface, its little fins splashing the waves. Nathan picked it up, discovering it was a girl, and set her down at her mother's side.

Achilles moaned in pain, managing to push the next pair out, both boys. They too were set at her side where at once they latched on and began to suckle. Despite her agony, Achilles managed a purr.

"I never thought I would feel that..." She rasped.

"Keep going, you've got nine more." Nathan encouraged.

Achilles' screams and wails sounded out for the next several hours as she labored to push the remaining pups out. She'd managed 7 before the remaining 5 decided they wanted a little more time in the womb and remained there. Achilles tried to push them out but they were resolute.

"They'll come when they are ready." Nathan told her. "In the meantime, try to rest. You've been at it for hours."

"So have you." She pointed out.

"I haven't just given berth to 7 babies." Nathan said.

Achilles gave in and rested against his hull. He gladly supported her. "I owe you one, Yank." She said.

"You owe me nothing, Brit." He shot back. "It's a ship's code to help another in distress."

Achilles licked her thanks and curled around her 7 pups, getting a few hours of peace.

2 hours later, she was at it again. The remaining five pups weren't eager to come out but they weren't resolute in not coming out either. Either way, Achilles couldn't keep this up for much longer. The submarine was exhausted. She'd been at this for 10 hours straight!

Finally, after 15 grueling hours, the last pup was finally born. Achilles collapsed against Nathan, 12 little bundles all squirming at her side. Their exhausted mother, wounds both external and internal beginning to get the better of her, curled up to go to sleep.

Nathan nudged her, doing what he could to keep her awake but he could only do so much. And no one had compatible blood for a submarine. That was unique to the submarine community alone.

"Achilles, stay awake." Nathan urged her as the sub began to nod off again.

"Mmm, can't." She managed. "Sleepy."

"I know. I know you're sleepy but you can't go to sleep now. You'll die." Nathan said.

"Death is what I deserve." She rasped. "Nathan, I never told you how grateful I am to you for helping me. I should've just been left to rot, like all the other people I'd left to do the same."

"That was the Ramsey's Achilles, not you." He said.

"I could've stopped them." She murmured. "Like I am doing now. They are closed off, all systems turned off. When I die, they die."

"There has to be another way. I'll carry you into a drydock. There are still people who can help." He said.

"Carry me, your and my 12 pups?" She asked. "You'd break your back trying."

"I can still try." He replied.

She shook her head. "In another life, I would've been proud to call you my friend." She rasped, holding out a fin.

Nathan didn't know what to say to that. He met the outstretched limb with a wire, grasping it tightly. "Achilles, please..." He begged, his voice breaking.

He'd lost so many, he couldn't lose another.

Achilles smiled, a warm but sad expression. She gazed at her pups. "They are strong and healthy and deserve a better mother than me. Take care of them. See they don't make the same mistakes I did."

"Achilles, I.." Nathan began.

"Promise me." The sub begged, her green eyes passionate.

Nathan could feel her hull growing cold. There was so little time. "I-I promise." He whispered.

She gripped his wire in her fin, resting against him. "Thank you, _sina._ " Her grip slackened and Achilles moved no more...


	13. Chapter 13 A More Perfect Union

Nathan wasn't sure what to expect as he entered St. Louis. A day had passed since Achilles' death and the destroyer was doing his best to soothe her hungry shiplings. They constantly wailed and whined, desperate for food. Rachel had made some milk for them with what she had in the medical stores but it wasn't much and it wasn't the kind of milk the pups needed. Nathan had to put into a port somewhere and stock up on stores of preserved sub milk.

He rounded a corner, weapons at the ready as he fully expected a civilian fleet to come at him with makeshift weapons blazing. Instead what he found were people cheering on the shoreline. As he passed by the Grand Arch he saw what ships had gathered in the harbor. He recognized a few. The young teenager Zumwalt. The massive carrier Enterprise, god knows how she made her way into the tight harbor. There were also the museum ships Yorktown, Laffey, and Clamagore. Nathan saw and bit back his whine of worry when he saw a familiar black hull huddled in a berth at the far end of the harbor. Thresher raised her head weakly to smile at him.

"Hey." She croaked.

Her black hull was covered in sores and she was hull and frame pretty much. Had no one bothered to feed her? Nathan approached her, having been given the contagious booster shot by Rachel. His shipling and the pups had their own immunity as well.

"Thresher." He whispered, resting his head over hers, exhaling on her.

She leaned into him, opening her jaws as she inhaled his scent. "I missed you." She rasped.

"I missed you too." He replied, brushing his lips across the top of her head. She purred, her head dropping as coughs wracked her. "You'll feel better soon." He whimpered.

"I know. Thank you, Nathan." She murmured.

She leaned back, resting a fin over her nose. Nathan smiled. "That's it. Rest." He murmured.

He backed off, turning to Clamagore. "I've got a dozen hungry pups and I don't have food for them." He said.

"Say no more, I've got 'em." The old sub smiled. "At least until Miss Wet Nurse over there gets better."

"Oi!" Thresher growled though there was a twinkle in her eye.

Nathan docked at his assigned berth, watching as his crew disembarked. The President granted Rachel a pardon and after he was inaugurated, he chose Chandler as his CNO. A big job to be sure but Nathan expected to be in drydock for months. A lot needed to be done in that time. He couldn't go to the presidential ball but Clamagore could. Submarines had the unique ability to shrink themselves down to a reasonable size making it easier for them to move about on land. Nathan and Thresher watched the pups while she was gone. The old submarine was getting better every day. The sores on her hull became less aggravated and she didn't have new ones breaking out. She'd stopped coughing up blood though she did occasionally break down in a fit. The vibrant sparkle in her green eyes had returned and she was getting some meat back on her thin frame. She looked up at Nathan from where she was licking one of the pups, Achilles named for her mother.

"She's distressed about something. I can't figure out what." Thresher said.

"Any idea why?" Nathan asked.

"Well I do know that most subs have what you could consider a sixth sense. We can tell when something's wrong or is about to go wrong. Before this whole epidemic started, there were worldwide reports of submarines getting increasingly highstrung and agitated, less willing to follow the rules of military discipline." She explained.

"I see and you think that something's wrong here?" Nathan questioned.

"Yes."

"Then why aren't you acting up?" Nathan asked.

"A valid question. In truth, I too sense something but I am more adapt at controlling my instincts than most. I have perfected my military discipline. Had to, if I was going to last as a spy." She answered.

The destroyer nodded. "Any idea as to what's wrong?" He asked.

"That, is something my senses cannot tell me." She sighed.

...

Thresher's senses proved to be deadly accurate. After the ball, Rachel came face to face with a stranger.

"Hello, can I help you?" She asked.

"Are you the lady who discovered the cure?" He asked, staggering forward with a slight limp. That and his ragged close made Rachel wonder if he was ill or had some family that was ill. Due to the lack of boils on his skin she suspected the latter.

"Yes, did you miss the initial reception?" She asked.

"Yes. I hear the cure is contagious. Uh how close do you need to get?" He asked, staggering forward all the while. Rachel could smell the alcohol on him and hid her wince.

At arms length, she drew the line. "That's close enough." She said.

He paused. "So long bitch." He grinned and raised an arm. In his hand was a gun. He pulled the trigger. The muzzle had a muffler on it so no one heard the gunshot.

Rachel gasped as she was shot in her left breast. She staggered against the wall, gripping the railing for support. The man turned and walked away and Rachel lacked any strength to go after him. Her right hand went up to her breast as her medical training kicked in. She had to stop the bleeding. She tore off part of her thin tights and pressed it to the wound, a better substitute than her hand. Blood still flowed though and there was no exit wound, meaning the bullet had lodged somewhere close to her heart. Her legs gave out and she fell on her knees, rolling on her back as her other hand let go of the railing and came up to hold the cloth over the wound. Numbness spread across her body and she tried to fight it but blood loss made her weak.

 _"Nathan, I'm sorry."_ She thought and everything went black.


End file.
